First of all, it's great that you take notes. That's a really nice habit to get into
You haven't mentioned your current water parameters...when was the last time you had your water tested and what method did you use?
Parasites are definitely a possibility. I looked into Aqua Flourish, though, and it doesn't seem to be an actual parasite treatment. Actually, it looks more like over-priced vitamins in liquid form to me.
Unfortunately, it's impossible to give a diagnosis without using a microscope to identify the parasite in question. If you have a veterinarian in the area that treats fish, now would be a good time to call them.
You could also try using a general anti-parasite treatment. The problem is that some may harm your plants.
Are you sure that no parasites are visible? Eyes, gills, fins, etc. look normal? A protozoan (maybe Coccidia?) is a possibility.
Windex wouldn't have caused a parasite to randomly appear in your tank. That makes no sense to me. However, if some Windex got into the tank by mistake then that could cause serious problems (and would kill shrimp pretty fast). If you suspect that the Windex is the cause then I would change most, if not all, of the water. You can leave the plants and gravel in, just change the water itself.
Leaving your tank fishless will not cause the cycle to die immediately or anything as long as you leave the plants, gravel, and water in the tank. So if you end up with no fish then maybe give it a few weeks before you get new ones. Some parasites will die in this amount of time because they can't find hosts. You could also add some aquarium salt and raise the temperature in this time period to further combat any parasites.
The pineconing seems to suggest internal bacterial infections, though. Either you have a couple problems going on at once or it's a simple infection that just wasn't treated correctly. The first step in either case is to get your water tested and do some water changes.
Actually, I just realized that you didn't mention what you've tried as far as treatments go. Have you tried anything yet? It might be a pretty simple problem.
Also, keep in mind that the guppies themselves might not have been healthy to begin with. Pet store livebearers are very inbred and tend to be kept in pretty crowded conditions.
Good luck and keep us updated!!